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Chapter 20 : Horizontal Gene Transfer and Prokaryotic Genome Evolution

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Abstract:

An early indication of the extent of prokaryotic horizontal gene transfer came from the multifactorial analysis of codon frequencies in portions of the genome that revealed significant deviations from the general pattern of codon usage in approximately 15% of this bacterium's genes. Comparative analyses of archaeal genomes presented particularly striking evidence that strongly suggests massive horizontal gene exchange with bacteria. Genomic era revelations of the widespread contributions of horizontal gene transfer to the gene composition of prokaryotic genomes amounted to a major shift in one's understanding of evolution. This chapter discusses the methodology used to infer horizontal gene transfer events and also discusses examples of such transfers among prokaryotes with an emphasis on adaptive and biological implications that they entail. From a pragmatic perspective, phylogenetic analysis is time- and labor-consuming because it depends critically on correct sequence alignments and is hard to automate without compromising the robustness of the results. The term "surrogate methods" was coined to describe methods of detecting horizontally transferred genes based on their anomalous nucleotide composition. The acquisition of eukaryotic genes by bacteria may be of particular interest because of the possible role of such horizontally transferred genes in bacterial pathogenicity. Eukaryotes have vastly more complex signal transduction systems than most bacteria and archaea. Horizontal gene transfer, particularly between eukaryotes and bacteria, emphasizes the remarkable unity of molecular-biological mechanisms in all life forms.

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
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Figures

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FIGURE 1

Distribution of the Clusters of Orthologous Groups of proteins (COGs) by the number of represented species. Each COG includes predicted orthologs from at least three genomes that belong to 26 distinct lineages. The number of COGs ( axis) is plotted against the number of phylogenetic lineages represented per COG axis). Adapted from .

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
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References

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Tables

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TABLE 1

Probable horizontal gene transfers detected using phyletic patterns

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
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TABLE 2

Probable interdomain horizontal transfers

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
Generic image for table
TABLE 3

Probable horizontal gene transfers between major bacterial lineages

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
Generic image for table
TABLE 4

Classification of candidate horizontal gene transfer events in selected genomes

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
Generic image for table
TABLE 5

Apparent phylogenetic affinities of eukaryotic best hits in bacteria and archaea

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
Generic image for table
TABLE 6

Horizontal transfer of eukaryotic aaRS genes into different bacterial lineages

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
Generic image for table
TABLE 7

Examples of eukaryotic-bacterial transfer of genes coding for proteins and domains involved in signal transduction

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20
Generic image for table
TABLE 8

Examples of eukaryotic-prokaryotic transfer of functionally diverse genes

Citation: Jordan I, Koonin E. 2004. Horizontal Gene Transfer and Prokaryotic Genome Evolution, p 319-338. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch20

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